variableSites: Variable Sites
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data
View source: R/variableSites.R
variableSites R Documentation
Variable Sites
Description
Identify variable sites among sequences.
Usage
variableSites(x, bases = c("a", "c", "g", "t", "-"), simplify = TRUE)
Arguments
x
a gtypes object with sequences,
a DNAbin object, or a list of sequences.
bases
character vector of bases to consider.
simplify
if there is a single locus, return result in a simplified
form? If FALSE a list will be returned wth one element per locus.
Value
A list with:
- site
a DNAbin object composed of variable sites.
- site.freqs
a matrix of base pair frequencies by site.
Author(s)
Eric Archer eric.archer@noaa.gov
See Also
fixedSites
Examples
data(dolph.haps)
variableSites(dolph.haps)
EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.
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View source: R/variableSites.R
| variableSites | R Documentation |
Variable Sites
Description
Identify variable sites among sequences.
Usage
variableSites(x, bases = c("a", "c", "g", "t", "-"), simplify = TRUE)
Arguments
x |
a gtypes object with sequences,
a |
bases |
character vector of bases to consider. |
simplify |
if there is a single locus, return result in a simplified
form? If |
Value
A list with:
- site
a
DNAbinobject composed of variable sites.- site.freqs
a matrix of base pair frequencies by site.
Author(s)
Eric Archer eric.archer@noaa.gov
See Also
fixedSites
Examples
data(dolph.haps) variableSites(dolph.haps)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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